Saved Souls
by FictionLover007
Summary: Alec has had enough. His family is torn apart, his parabati is filled with Heavenly Fire, and his boyfriend left him. He's got nothing left to lose, so he volunteers to do something very dangerous; become a double-spy for the Clave. Warnings: M/M slash, Malec, Sebalec, Sizzy, Clace, possible m!preg, pre-City of Heavenly Fire/CoHF, and possible CoHF spoilers.
1. Chapter 1

**So this is my second Mortal Instruments story, but this is the first multi-chapter, so bear with me. Disclaimer: I'm not Cassandra Claire, I wouldn't be making fanfiction if I was. **

**Alec's POV**

I stared at my phone in misery. Magnus had broken up with me three days ago, and yesterday I had been summoned to the Alicate. There was to be a meeting. Sebastian had attacked an Institute, and the Clave needed a plan. All adults were required to attend, and that unfortunately included me.

I stood at the back of the room as the Council talked strategy, and a thought occurred to him. _What Jace wouldn't give to be here right now. _But Jace wasn't here. He was with the Silent Brothers, who were still trying to figure out how to separate the Heavenly fire from his soul.

Izzy was probably with Simon, back in New York, and Clary was with Jocelyn, helping with the wedding plans. _I wonder what Magnus is doing?_ No, Alec, you can't think about him. Ever. He broke up with you and you need to get over him.

My mind snapped back to the meeting, when Jia Penhallow announced "The only thing that would allow us to know what Sebastian intends to do would be if we had a spy within his ranks. Someone he could believe would betray the Clave." Murmurs echoed throughout the room, and I had an idea.

"I could do it." Eyes turned towards me. Jia looked me in the eyes and said "What makes you think you could do such a thing, Mr. Lightwood?" I smiled and said "My parents associated with his father, who's to say that there wasn't an underlying feeling of rebellion about the Lightwood household when I was born and on top of a recent break-up, I'm not feeling partial to New York at the current moment. And it's not like I can go out hunting with my parabati the way he is. I might be a bit frustrated and a bit angry. I might see him as a better choice, perhaps."

The Consul looked thoughtful. "And what's to say you won't sell us out to Sebastian, Mr. Lightwood?" I looked confused. "Why would I do that? Sebastian killed my brother, I want to do my part in avenging him." The Consul looked out over the room. "Are there any other volunteers?" No one said anything.

Jia looked at me and said "Well, Mr. Lightwood. How do you plan to ascend to Sebastian's ranks then."I need to be at the next Institute he will attack. Do you know which one it is?" "The Los Angeles Institute is on the list, we believe." "Then I need to go to Los Angeles, and join Sebastian's ranks there." "Are you sure?" "Consul, do I really have a choice at this point." "No, no you don't."

_Time Skip_

"Mr. Lightwood! Welcome to California." I looked at the man in front of me. "Mr. Carstairs, I presume?" "That's correct, but please, call me John." "Well in that case, please call me Alec." "Well, welcome Alec, and may I introduce my daughter, Emma." "Hi Alec!" "Hello Emma." John cut in again. "Well, let me fill you in on the situation. The rest of the institute has been evacuated, as per your instructions, and the fake weapons made by the Iron Sisters in the armory." "Great, and the protective runes on the library?" "Yes, those have been done as well." "Um, I have a question, Alec?" "Yes, Emma?" "Why isn't your parabati with you?" "My parabati?" "Yeah, Jace Wayland Lightwood Herondale Morganstien?"

I raised my eyebrow at the twelve year old girl. She blushed and turned her head.i shook my head mentally at Jace. "My parabati is a bit of a drama queen and wasn't too happy about my volunteering for this whole "joining Sebastian" thing." She giggled, and I smirked knowing Jace would take offense to the "drama queen" statement. But then I remembered his reaction when I told him.

_Flashback_

_"Are you crazy? Alec, you will be killed!" "Jace, listen to me. I can do this." "Really? Because Alec, for the past three days, you've been crying over a break-up, and now you want to be a double agent pretending to side with the man who killed Max." "I know that, but Jace, I'm the best person for the job, and the break-up is part of the cover story. And besides, I know how to handle myself in a fight." "Alec, he beat me." "And so have I." "In practice!" "So? You weren't exactly holding back." "A lot has changed since then." "I know, so have I. Jace, I have to do this." "No, you don't." "Jace, I'm going to do it." "But..." "No, Jace, I'm doing this, and besides, I'm older, you can't tell me what to do." _

_He looked at me in shock. "Don't tell me you waited seven years to pull the age card." "I did." "Ugh, fine. Just... Come back alive, okay. Izzy would kill me if you didn't. Speaking of Izzy..." "I planned on telling her the day before I leave." "When's that?" "I leave next week, if the Institute isn't attacked before then." "She's still gonna kill me anyway, for letting you go isn't she." "She'll kill us both, and then probably take her anger out on Simon." _

_He smiled and agreed. "You should tell her sooner, give her a chance to say good..." He cut off, refusing to finish the sentence, knowing that if he did, he wouldn't be able to look his parabati in the eye. "Chance to say goodbye, if I don't come back." Jace flinched when I finished the sentence for him. I put my hand on his shoulder and looked him in the eye. "I'll come back. I will, I promise." He sighed, and said "If you don't, I will find a way to resurrect you and kill you myself. Got it?" I nodded and I smiled at him. _

I snapped back to the present, and I wondered what Jace was doing. I wished I could send him a message, but I couldn't. I had to make it look like I was estranged or my cover wouldn't work. I just hoped it would.

**So let me know what you think, anyone who reads this. Should I continue this or abandon it? Just press the little blue button, come on, you know you want to! **


	2. Chapter 2

Alec's POV

On the day Sebastian came, Emma Carstairs lost her father. So did her best friend, Julian Blackthorn.

The weather outside had been beautiful. Much better than New York winter days. I stood out on a balcony, watching the sun. I wore a loose fitting black tank top and grey cargo pants. Knives were slotted into holsters held at the small of my back and in both combat boots.

I watched the clouds as the rolled by, the palm trees as they waved in the wind. The sea sparkled as if waves of turquoise glitter was floating on the surface. _Magnus would love this._ I couldn't help but think of my ex-boyfriend at a time like this. By the Angel, I missed him. I wished I had more time with him, but my own insecurity tore us apart. I wondered if he knew what I was doing right now, and if he missed me at all. He probably didn't. He probably hated me.

I was still thinking on this when I saw someone standing in the middle of the road. It was a shadowhunter in red robes, an Endarkened warrior. I rushed back inside, only in time to see Sebastian burst through the doors. I had no blades drawn and Sebastian stepped forward.

"Alexander Lightwood. What are you doing here?" I took a deep breath and said "I wish to swear allegiance to Jonathan Morganstien. I do not wish to serve the Clave any longer, and be denied the chance to become better and be free of the corrupted hold they keep firm upon me. I also wish this freedom upon the two children I carry within me."

Sebastian stepped forward. "And how is it possible, that you, a male shadowhunter, can bear children?" "I am a bi-gender being. The ability is passed down through heritage, and it passed to me. It was created in case shadowhunters ever began to die out as a race. Of course, when it was created, it was unthinkable of a shadowhunter to lie with a warlock."

Sebastian looked even more interested. "A warlock? Which warlock?" "Magnus Bane." "How do I know you do not lie?" Let me stick around with you for a month, if you see no baby bump, you may kill me, if you do, you will know I do not lie. I would even swear upon the Mortal Sword, but alas, you don't have it."

He was clearly playing with the idea in his head, but there was something stopping him. "Why did you leave your parabati?" "He is ill, with Heavenly Fire in his veins. He harms those around him, he has already harmed Clary. I fear for my children."

"He harmed Clarissa?" There was a hint of anger in his voice. "They both spoke of it as an accident, but he has a lot of those. Mark my words, his accidents have ended up with someone hurt more times than he would care to admit. Many of those times, it has been me injured, but no more."

"Well, Alexander, welcome to my brotherhood." I approached and two Endarkened escorted me out of the Institute. I smiled to myself. That was the easy part, over with. Time to move to Phase II of my plan.

As we moved out, Sebastian opened a portal, and the Endarkened stepped through. He turned to me, and held out his hand to me. I didn't hesitate, I took his hand and we stepped through, together.

-3 months later-the New York Institute-

"Ladies and Gentlemen, we have convened here to discuss a troubling matter." "Is there a reason, Consul, I have been summoned to a shadowhunter meeting?" "Yes, Warlock Bane, there is." "And what may that be?" "Warlock Bane, what is the probability that you could have sired two warlock children?" "Excuse me?" "I will not repeat myself." "The chances of me fathering one, let alone two, children are 1 in 50." "Then, Ladies and Gentlemen of the Counsil, we need to decide. All those in favor of terminating the twin children of Alexander Lightwood and Jonathan Morganstein once they are born, say aye." "Aye!"

The affirmative response to the vote resounded throughout the room. Some shook their heads, unaccustomed to the idea of killing a child of a shadowhunter. Some didn't do anything, choosing to not participate. "Those that say nay, speak now." There was silence.

Magnus was shocked. Alec was having children with Sebastian? How? When had Alec joined Sebastian? Had their break-up driven him to do it? Guilt surged through the warlock, and then he saw Jace.

The blond shadowhunter looked furious. But he wasn't looking at Magnus, he was glaring at the Consul. If looks could kill, the Consul would be less than a pile of ashes that was still on fire. Magnus decided to risk his life and talk to him.

"Hello Jonathan." "Warlock Bane." "If I may ask, no one will explain the situation to me, because no one else will. What is this about Alexander having a child?" "Children. He's having twins." "Excuse me?" "Alec can bear children. All firstborn Lightwoods can, it's a passed-down trait. And now he's pregnant, with twins. Maryse reckons that he's maybe three to four months along. Which is why you were called in. Three months ago, Alec started something. He's joined Sebastian in an attempt to get close to him. Now, what has happened is that Alec was spotted, in Rio, with a bow on his back, and a baby bump on his front. Too big for one baby for how far he is along, which leads to believe he's having twins. But what we don't know is who the father is. The Clave has narrowed it down to you or Sebastian. There's no reason for Alec to be involved with anyone else."

"If it was me, why wouldn't Alec have told me?" "Would you have listened if he did? He was gone a week and a half after you two broke up. If he was pregnant then, he didn't tell anyone. If he tried to tell you, you weren't picking up the phone."

Magnus had guilt written over his face. He felt bad for driving Alexander to perform such a dangerous task, not listening when he needed Magnus more than anything, and for breaking up with him in the first place. He regretted it. But he also deserved it, to lose Alexander. Alexander didn't deserve this. He straightened and turned.

"Where are you going?" Jace called out to Magnus. Magnus faced him and looked him in the eye as he said "I'm getting him back." Jace raised an eyebrow. "And how are you going to do that?" "I'm going to visit my father." With that, Magus walked away, not noticing Jace, Clary, Isabelle, and Simon follow him.


	3. Chapter 3

"Asmodeus is a greater demon and was once an angel but he fell, and he's your FATHER?" Isabelle screeched.

"Yes."

"And you couldn't mention that to Alec?"

"It wasn't relevant."

"Relevant? Now I know why he went to Camille."

"Why?"

"Well, it's obvious. Even I know that a relationship can't survive long without sharing."

"We shared an apartment."

"Information, Magnus, information. About your past. Which Camille had."

"I shared that too. I told him the story about how I started dressing in sparkles, and..."

"By the angel, that's not the point. The point is sharing the real stuff. I'm willing to bet that you know everything about Alec."

"Yes, but..."

"Uh uh, I'm talking."

Magnus rolled his eyes at the female Shadowhunter. She shot him a glare and continued.

"How much did Alec know about your ex's, past interests, past places where you lived, your family history?"

"Well, he knows that..." "He doesn't know a thing does he?"

Magnus dropped his head in defeat. "No."

"No, he doesn't. So why..."

"Drop it Isabelle." Jace cut in. "This isn't helping us get Alec back, so stop it. Magnus, what's your plan? Why do you need to talk to Asmodeus?"

"He knows the location of where Sebastian is hiding, and Alec too if they're together. I can find Alec and get him out of there before the Clave decides to kill him, and the babies."

"Well, then, you aren't going alone."

"Oh Jonathan, I'm not going anywhere. Asmodeus is coming here, to the Institute."

Isabelle raised an eyebrow. "Here? Why? More importantly, how?"

"I intend to summon him, here on consecrated ground."

"I'm assuming you have bigger issues with your father than Alec has with ours?"

"Something like that."

"Then why would he help you?"

"He will be very interested in a child between a warlock and a shadowhunter. That shouldn't even have been possible."

"What if Sebastian is the father?"

"Then may Raziel burn us all."

"That's a comforting thought."

-Somewhere in Hell, Jonathan paced up and down a corridor outside a pair of double doors, waiting. He did not like to be kept waiting, but he supposed that in some situations, the proverb "Good things come to those who wait" applied to his benefit.

The doors opened and a warlock stepped out. She was a supporter of his, and he needed her input on the matter of Alexander.

"Well?"

"The warlock's children are strong, as is their parental host. A boy and a girl, healthy, and maturing normally. I would suggest that the operation does not take place until Alexander is halfway through his third trimester at the earliest, but I would recommend waiting until the third trimester is up."

"They may not survive until the end of the third trimester, I need them to survive."

"For your cause?"

Jonathan hesitated. "Yes...uh, for my cause."

"Very well. You may see him if you wish."

He nodded. "You are dismissed."

The woman scuttled away and Jonathan walked through the doors to find Alec Lightwood struggling to pull on a t-shirt over his now prominent five-month old baby bump.

"Oh, Jonathan, I didn't expect you."

"I know. Would you like some help?"

The boy blushed. Pretty, Jonathan thought.

"Yes, please. With the bump putting a strain on my back I can't lift my arms well."

Jonathan moved over to the eighteen year old, noting the faint scars littering his back, ribs, stomach, and arms. Leftovers from fights with Downworlders and monsters, runes carved into his pale skin. He also noted that he could count every bone in his ribcage.

"You aren't eating enough." Jonathan slipped the arm hole over Alek's hand, and up his arm. The young boy shivered.

"What makes you say that?"

"You may be pregnant, but you are too skinny."

"I...I am sorry."

"Don't be. But you must take care of yourself Alexander."

Alec flinched. Jonathan noticed.

"Is something wrong? Did I hurt you?"

Alec shook his head. "No, it's nothing."

"You're lying."

Alec sighed, and said "Magnus used to call me Alexander. He was the only one who did it out of kindness, and it made me trust him. But when he cut me out, he used it in anger, and now, every time I hear my full name, I just..."

He didn't finish the sentence, but his eyes said the rest. "You wish that someone would not abuse the right to call you that."

He nodded. "Would you like me to use Alec instead?"

He bit his lip, and said "For now. At least until the babies are born, and then, we'll see about Alexander."

"Speaking of names, and the babies, have you chosen their names yet?"

He nodded. "The boy's name will be Henrietta, and the boy's name will be Charles, Henri and Charlie for short."

"May I ask why?"

"Long ago, my ancestor, Gideon Lightwood, met the mundane who would ascend to be his wife, Sofie, at the London Institute, headed by the first woman to be in charge of an institute. Her name was Charlotte Branwell, and she became the godmother to Gideon and Sofie's son. My great-grandfather. Charlotte's husband, Henry, was a brilliant Shadowhunter scientist, and worked closely with the Iron Sisters and the Silent Brothers, to create the first portal. I was almost promised to marry their descendant, Lydia. But she married a few years ago, and moved to Rio, I think. That's where I got the names Charlie and Henri, they are the opposite gender names to Charlotte and Henry."

"What about middle names?"

"James and Theresa maybe, but I haven't really thought about it."

"Maybe Jonathan and Isabelle for middle names, after your parabati and sister?"

Alec smiled at Sebastian, and Sebastian didn't understand the flutter in his stomach.

"I like that. Thank you Jonathan."

"You are most welcome, Alec."

A.N. So, I kind of...forgot about this story, until I found a half-written chapter on my phone, and I thought I would continue it. I'm still not sure who Alec is going to end up with, but I may write two endings, one with Sebastian and one with Magnus, if you guys want. Hope you enjoyed the chapter, and I will try not to take two years to update this again. Bye bye!


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